Sliding Windows Analysis

Weird Populations, Size 50kb step 10kb

EGL_LkC_plot <- ggplot(data = EGL_LkC, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = EGL_LkC_axis_set$chr, 
                     breaks = EGL_LkC_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(EGL_LkC_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "East Grand L. vs L. Champlain", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
EGL_LkC_plot

EGL_PtL_plot <- ggplot(data = EGL_PtL, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = EGL_PtL_axis_set$chr, 
                     breaks = EGL_PtL_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(EGL_PtL_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "East Grand L. vs Pattagansett L.", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
EGL_PtL_plot

EGL_QnL_plot <- ggplot(data = EGL_QnL, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = EGL_QnL_axis_set$chr, 
                     breaks = EGL_QnL_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(EGL_QnL_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "East Grand L. vs Quonnipaug L.", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
EGL_QnL_plot

EGL_RgL_plot <- ggplot(data = EGL_RgL, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = EGL_RgL_axis_set$chr, 
                     breaks = EGL_RgL_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(EGL_RgL_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "East Grand L. vs Rogers L.", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
EGL_RgL_plot

EGL_RnR_plot <- ggplot(data = EGL_RnR, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = EGL_RnR_axis_set$chr, 
                     breaks = EGL_RnR_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(EGL_RnR_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "East Grand L. vs Roanoke R.", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
EGL_RnR_plot

PtL_QnL_plot <- ggplot(data = PtL_QnL, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = PtL_QnL_axis_set$chr, 
                     breaks = PtL_QnL_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(PtL_QnL_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Pattagansett L. vs Quonnipaug L.", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
PtL_QnL_plot

PtL_RgL_plot <- ggplot(data = PtL_RgL, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = PtL_RgL_axis_set$chr, 
                     breaks = PtL_RgL_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(PtL_RgL_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Pattagansett L. vs Rogers L.", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
PtL_RgL_plot

RgL_QnL_plot <- ggplot(data = RgL_QnL, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = RgL_QnL_axis_set$chr, 
                     breaks = RgL_QnL_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(RgL_QnL_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Rogers L. vs Quonnipaug L.", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
RgL_QnL_plot

RnR_LkC_plot <- ggplot(data = RnR_LkC, 
                       mapping = aes(x = pos_cum, 
                                     y = Fst, 
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = RnR_LkC_axis_set$chr, 
                     breaks = RnR_LkC_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(RnR_LkC_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Roanoke R. vs L. Champlain", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
RnR_LkC_plot

RnR_PtL_plot <- ggplot(data = RnR_PtL,
                       mapping = aes(x = pos_cum,
                                     y = Fst,
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = RnR_PtL_axis_set$chr,
                     breaks = RnR_PtL_axis_set$center) +
  scale_y_continuous(expand = c(0,0),
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"),
                                  unique(length(RnR_PtL_axis_set$chr)))) +
  labs(x = NULL,
       y = "Fst",
       title = "Roanoke R. vs Pattagansett L.",
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
RnR_PtL_plot

RnR_QnL_plot <- ggplot(data = RnR_QnL,
                       mapping = aes(x = pos_cum,
                                     y = Fst,
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = RnR_QnL_axis_set$chr,
                     breaks = RnR_QnL_axis_set$center) +
  scale_y_continuous(expand = c(0,0),
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"),
                                  unique(length(RnR_QnL_axis_set$chr)))) +
  labs(x = NULL,
       y = "Fst",
       title = "Roanoke R. vs Quonnipaug L.",
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
RnR_QnL_plot

RnR_RgL_plot <- ggplot(data = RnR_RgL,
                       mapping = aes(x = pos_cum,
                                     y = Fst,
                                     color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = RnR_RgL_axis_set$chr,
                     breaks = RnR_RgL_axis_set$center) +
  scale_y_continuous(expand = c(0,0),
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"),
                                  unique(length(RnR_RgL_axis_set$chr)))) +
  labs(x = NULL,
       y = "Fst",
       title = "Roanoke R. vs Rogers L.",
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
RnR_RgL_plot

### Using ggsave to save the manhattan plots, or as I will now refer to it: ###
# Saving Private Plots (Ryan lol) ##
ggsave("figures/sliding-windows-fst/MIDA-x-NATLA-sz50-chrom19-spike.png", 
       plot = mxn50_chr19_spike_plot, 
       width = 10, 
       height = 4)